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Lecture 2

Lecture 2 - Sept 10.pdf

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Department
Biology (Sci)
Course
BIOL 200
Professor
Richard Roy
Semester
Fall

Description
2012$09$10& BIOL200 Lecture 2 - Sept. 10 DNA & RNA: “Backbone” is composed of repeating phosphate-pentose units (C,A,G) • • Has end-to-end orientation or bias B DNA can bend about its long axis • 5’ end - free phosphate group on the 5’ carbon of the terminal sugar • 3’ end - free hydroxyl on the 3’ carbon of the terminal sugar Important in DNA-protein interactions and in DNA denaturation andnucleotides covalently bonded is through phospho-diester the folding of DNA into compact condensed bond structures r•nSince DNA and RNA synthesis proceeds in a 5’ to 3’ direction, nucleic acids are during DNA replication and in 5’ to 3’ (i.e. 5’-CAG-3’)s • DNA contains two polynucleotide strands woundsed of tratogether to form a double helix repeating phosphate- exploited in many techniques Sugar-phosphate backbone on the outside of thee units in molecular biology and double helix g•nomics.stack on top of another forming parallel planes • Orientation of the polynucleotide strands in the double helix is antiparallel; one goes from 5’ to 3’ while the other goes from 3’ to 5’ • Base pairs to form Watson-Crick base pairs (bp) •T = A (2 hydrogen bonds) •G ≣ C (3 hydrogen bonds) •A = T (2 hydrogen bonds) C ≣ G (3 hydrogen bonds) • DNA denaturation or melting and T m •Base complementarity •Stabilizes double helix primarily by H-bonds ▯ between bases •A purine must be complementary to a pyrimidine •Most DNA in cells is a right-handed helix Tmis a B, A, & Z Form of DNA: • Two helical grooves, the major and minor grooves, allow DNA-binding proteins to interact with the double helix In very low humidity (and dehydrated samples), the B form of DNA changes to the A form • • In addition, RNA-DNA and RNA-RNA helices exist in the A form • Short DNA molecules of alternating purine and pyrimidine nucleotides adopt a left-handed helix conformation known as the Z form. Z DNA is also transiently formed shortly after transcription and, as such, is a tag for actively transcribed genes • B DNA can bend about its long axis. This is important in DNA-protein interactions and in the folding of DNA into compact condensed structures • DNA denaturation and renaturation is important during DNA replication and in transcription. It is also exploited in many techniques in molecular biology and genomics • Tmis a function of G ≣ C content due to the extra hydrogen bond requiring more energy to break the bond T ms a function of G•C content RBases stack on top RNA Structure: of another forming parallel planes Proteins: • Function is derived from the three-dimensional structure, and the three-dimensional structure is specified by the amino-acid sequence • Three-dimension structure = conformation Hierarchical Structure of Proteins: • Primary (sequence) is a linear amino acid sequence of the polypeptide • Has amino end (N-terminus) and carboxyl end (C- terminus) • Secondary (local folding) is similar to folding of RNA • Alpha helix and Beta sheet • Folding of localized regions of a polypeptide chain • Stabilizing non-covalent interactions forming, for instance: • Alpha helices Hierarchical structure of • R groups point outwards • Beta sheets Laterally packed beta strands. Beta strand = • proteins short, 5 to 8 residues, nearly extended polypeptide segment • H-bonding between backbone of the beta strands • Directionality - parallel (same orientation) or antiparallel (opposite orientation)
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